Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison

Results: HTML CSV LaTeX

Showing element 3708 to 3757 of 29840 in total

Interaction Map

: High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
232	melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]	Rooted	Divided	1	137.446	120.823	1.13758
	myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055]	Rooted	Subtracted		95.0526	85.3206	9.732
	rho-gtpase-activating protein 7 (rho-type gtpase-activating protein 7) (deleted in liver cancer 1 protein) (dlc-1) (hp protein) (star-related lipid transfer protein 12) (stard12) (start domain-containing protein 12). [swissprot;acc:q96qb1]	Squared	Divided		42411.6	55802.1	1.31573
	smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527]	Ranked	Divided		239.336	267.879	1.11926
	udp-n-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase (ec 2.7.8.15) (gpt) (g1pt) (n-acetylglucosamine-1-phosphate transferase) (glcnac-1-p transferase). [swissprot;acc:q9h3h5]	Measured	Subtracted		9649.61	11053.5	1403.89
233	60s acidic ribosomal protein p1. [swissprot;acc:p05386]	Ranked	Divided	0	9586.97	10560	1.1015
	60s ribosomal protein l15. [swissprot;acc:p39030]	Rooted	Subtracted	0	19.482	17.0546	2.4274
	60s ribosomal protein l7. [swissprot;acc:p18124]	Ranked		1	235.727	259.984	24.257
	aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468]	Measured		0	6158	6303	145
	ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447]	Squared	Divided	0	5294.83	3966.41	1.33492
	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042]		Subtracted	1	41502.9	30836.8	10666.1
	histone h2b.e (h2b/e). [swissprot;acc:q99879]		Subtracted	0	7090.8	7294.33	203.53
	huntingtin interacting protein c. [refseq;acc:nm_012272]	Rooted	Divided	0	22.1446	19.7536	1.12104
	lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461]	Ranked		1	239.32	267.842	1.11918
	maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168]	Measured		0	348.823	399.534	1.14538
	map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [swissprot;acc:p49137]	Squared		1	42411.6	55802.1	1.31573
	melanoma antigen, family b, 6. [refseq;acc:nm_173523]	Rooted			137.446	120.823	1.13758
	myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882]	Rooted	Subtracted		95.0526	85.3206	9.732
	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3]	Measured	Divided		9035	7279.6	1.24114
	rho-gtpase-activating protein 7 (rho-type gtpase-activating protein 7) (deleted in liver cancer 1 protein) (dlc-1) (hp protein) (star-related lipid transfer protein 12) (stard12) (start domain-containing protein 12). [swissprot;acc:q96qb1]	Measured	Subtracted		9649.61	11053.5	1403.89
	ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464]	Ranked		0	10367	9320.25	1046.75
234	40s ribosomal protein s23. [swissprot;acc:p39028]			1	243.944	268.195	24.251
	chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0]		Divided	1	287.41	256.835	1.11905
	guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148]	Rooted	Divided	0	16.0012	17.8885	1.11795
	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041]	Squared	Subtracted	1	41502.9	30836.8	10666.1
	histone h2b.c (h2b/c). [swissprot;acc:q99880]	Squared		0	7091.16	7294.68	203.52
	keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191]	Measured		0	1224.65	1079.77	144.88
	map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [swissprot;acc:p49137]	Measured		1	9649.61	11053.5	1403.89
	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]	Rooted	Divided		137.446	120.823	1.13758
	myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883]	Rooted	Subtracted		95.0526	85.3206	9.732
	myosin light chain 1, embryonic muscle/atrial isoform (pro1957). [swissprot;acc:p12829]	Squared	Divided	0	5294.83	3966.41	1.33492
	neuronal acetylcholine receptor protein, alpha-6 chain precursor. [swissprot;acc:q15825]	Squared		1	42411.6	55802.1	1.31573
	ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424]	Measured		1	5181.2	6410.58	1.23728
	suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169]	Rooted	Subtracted	0	27.1299	29.5494	2.4195
	transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [swissprot;acc:p15884]	Ranked	Divided		16614	18296	1.10124
	u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695]	Ranked	Subtracted		7502.08	6461.83	1040.25
	wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [swissprot;acc:q9upy6]	Measured	Divided		5202.89	4550.64	1.14333
235	28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235]	Ranked	Subtracted	1	243.944	268.195	24.251
	40s ribosomal protein s29. [swissprot;acc:p30054]	Ranked		0	11035.3	9997.71	1037.59
	atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [swissprot;acc:o76031]	Squared			1326.34	1126.71	199.63
	collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400]	Measured			2113.27	2255.28	142.01
	cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187]	Rooted			14.2752	16.6919	2.4167
	dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430]	Rooted		1	95.0526	85.3206	9.732
	elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [swissprot;acc:p04720]	Ranked	Divided	0	14554.5	16027.9	1.10123
	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043]	Squared	Subtracted	1	41502.9	30836.8	10666.1
	integrin beta-3 precursor (platelet membrane glycoprotein iiia) (gpiiia) (cd61 antigen). [swissprot;acc:p05106]	Measured	Divided	0	1612.86	1843.92	1.14326
	melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]	Rooted	Divided	1	137.446	120.823	1.13758
	neuronal acetylcholine receptor protein, alpha-6 chain precursor. [swissprot;acc:q15825]	Measured	Subtracted		9649.61	11053.5	1403.89
	nitrogen fixation cluster-like. [refseq;acc:nm_014301]	Squared	Divided		42411.6	55802.1	1.31573
	phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439]	Ranked	Divided		227.357	254.15	1.11785

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.

- http://analysis.yellowcouch.org/